annotate tools/emboss_5/emboss_megamerger.xml @ 0:9071e359b9a3

Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
1 <tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
2 <description>Merge two large overlapping nucleic acid sequences</description>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
4 <command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
5 <inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
6 <param format="data" name="input1" type="data">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
7 <label>Sequence 1</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
8 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
9 <param format="data" name="input2" type="data">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
10 <label>Sequence 2</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
11 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
12 <param name="wordsize" size="4" type="text" value="20">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
13 <label>Word size</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
14 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
15 <param name="prefer" type="select">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
16 <label>Prefer first sequence when mismatches occur</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
17 <option value="no">No</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
18 <option value="yes">Yes</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
19 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
20 <param name="out_format1" type="select">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
21 <label>Output Sequence File Format</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
22 <option value="fasta">FASTA (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
23 <option value="acedb">ACeDB (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
24 <option value="asn1">ASN.1 (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
25 <option value="clustal">Clustal (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
26 <option value="codata">CODATA (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
27 <option value="embl">EMBL (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
28 <option value="fitch">Fitch (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
29 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
30 <option value="genbank">GENBANK (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
31 <option value="gff">GFF (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
32 <option value="hennig86">Hennig86 (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
33 <option value="ig">Intelligenetics (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
34 <option value="jackknifer">Jackknifer (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
35 <option value="jackknifernon">Jackknifernon (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
36 <option value="mega">Mega (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
37 <option value="meganon">Meganon (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
38 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
39 <option value="pir">NBRF (PIR) (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
40 <option value="ncbi">NCBI style FASTA (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
41 <option value="nexus">Nexus/PAUP (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
42 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
43 <option value="phylip">PHYLIP interleaved (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
44 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
45 <option value="selex">SELEX (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
46 <option value="staden">Staden (s)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
47 <option value="strider">DNA strider (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
48 <option value="swiss">SwisProt entry (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
49 <option value="text">Plain sequence (s)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
50 <option value="treecon">Treecon (m)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
51 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
52 </inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
53 <outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
54 <data format="fasta" name="out_file1" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
55 <data format="txt" name="out_file2" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
56 </outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
57 <code file="emboss_format_corrector.py" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
58 <help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
59 You can view the original documentation here_.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
60
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
61 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/megamerger.html
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
62 </help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
63 </tool>